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List of Scientific Inaccuracies
NOTE: This game seems to be no longer under active development. The author of the game, John Halter, has failed to provide continued updates on the development of the game and to forfill his obligations to the Kickstarter backers. The information below is provided for historic reasons. Since this is a game which is inspired by microbiology (as opposed to a microbiology simulation), there are a couple of features which are scientifically innaccurate. These innaccuracies are in the game for a couple of reasons : #Fun - that is the main purpose of the game is for you to have fun. #Speed - the game needs to run reasonably well, so not everything can be simulated reasonably. #Ignorance - the maker of the game (me...John) doesn't know everything about microbiology, so there is a chance his ignorance added some innaccuracies into the game. #It's a game #Simplicity - the game is complicated enough, and some scientific principles make the game too complicated. Simple as that. #Time - It takes time to put in every microbiology concept into a game, and to correct every error. #Did I mention it's a game? Genetics Genes Many (almost all) genes in the game are not actual genes, but many represent actual genes. Some single genes in the game represent functions in the bacteria which require multiple genes. Metabolism genes, are actually more representative of metabolism operons, which are a specific collection of genes. Probably the most inaccurate genes in the game are the metabolism genes. Where one gene in the game handles various functions and nutrients, real metabolism takes multiple genes to handle a single nutritient. Synthesis Genes In the game there are two synthesis genes which are not including in the default bacteria, but are extremely common and important to all bacteria. These two genes are the nucleotide synthesis and protein synthesis genes, which the anologous real genes provide an important role for all bacteria. The reason they are not in the default starting bacterium in the game, is they are powerful genes which make survival easier, and therefore you have to work to get them. No In/Del mutations In/Del is short for insertion/deletion mutations, which is the insertion or deletion of a nucelotide in the genome. In/del mutations can be bad for an organism because it causes a frame shift which can destroy the function of the gene. They are not in the game, because they would cause problems in the code similar to a frame shift, which would crash the game at random. Of course code could be made to fix these crashes, but it currently isn't worth the trouble. Central Dogma The Central Dogma of Molecular biology is the fact that DNA makes RNA which makes Protein (at it's simplest). This game takes a slight variation on that where DNA makes a number which represents the protein. The process still uses codons, but the main difference is no RNA intermediate, and that proteins in real life don't have a numerical value. Stop Codon In real life there are 3 stop codons (TAG,TAA, and TGA), in the game only one is used (TGA). Single Stranded Real DNA is double stranded, meaning for a string of nucleotides there is a complementary strand. In the game the DNA is a string of letters, and a complementary strand is not made or used. Limitation on mutations There are certain areas on genome which don't mutate, these are functional regions for the coputer to use, so the computer can read the code properly. There is also a limitation on how large the genome gets (10,000 nucleotides long), because the larger the genome the longer it takes for your computer to analyze it. Regulatory Region In a gene, the region which regulates the control and expression of when the gene is used is in front of the ATG start codon. In this game, that region (which is also used to identify the gene), is after the ATG start codon. This is because it's somewhat faster for the computer, and cleaner code (but that would not be the case if it were to happen in life). Of course there is a way to make a program which has this region before the ATG, but the 'if it aint broke don't fix it' rule is in place, and this is such a small inaccuracy which has no effect on gameplay. Plasmid Dominace In the Game, a gene on a Plasmid immediately dominates a gene on the chromosome. In reality this doesn't always happens and is often more complex than the plasmid gene taking over the phenotype of the bacterium. Evolution Natural Selection Only a small range of the world is actually simulated. Simulated = contains nutrients and moving bacteria. The natural selection code can only act in the range of the simulation. All bacteria not in this simulated range does not have natural selection acting on them, and a slower, less scientifically accurate code for evolution takes its place in handling the bacteria out of the simulated range. Basically, only the simulated range around your bacteria does natural selection act on. The rest of the world is less scientifically accurate. Pre-game Evolution Before a new game begins, every species goes thru a simulated evolution history. This code was not made to be accurate in how evolution works, but only be accurate in the producing what bacteria which have undergone years of evolution would be like. Evolution Rate The rate of mutation in the game is higher than naturally found for bacteria. The rate of evolution, as far as how many mutations happen per copy of the genome, is more like the mutation rate of a virus (specifically HIV). Health The concept of health in the game was completely made up for the game. Bacteria don't exactly age, and when a bacteria divides, the 'new' cell doesn't gain more life. In fact there is no new cell and old cell, a more accurate statement would be two new daughter cells. These two daughter cells can then go on to divide, in that way bacteria are immortal. The reason there is an old cell/ new cell model in the game, is it adds tension to the game. And health cannot be picked up from the environment, like in the game. Speed Bacteria in the game can move around 1 body length per second. Real bacteria can move around 10 body lengths per second, but some can travel as fast as 100 body lengths per second. Rotation (Tumbling) When rotating a bacteria in the game, you get to control the direction it rotates. When real bacteria tumble, they don't control the direction they rotate, they just tumble about. You are given control over the direction of the bacteria rotation for fun and to remove frustration. Movement Only flagella based motility is represented in the game. But bacteria have alternative ways of movings such as gliding. Bacteria Shapes There are a couple of bacteria shapes in the game which are inaccurate an not foun in nature. They're in the game for fun and they look insteresting. Their design is still based on bacteria morphologies. Drift (No Brownian Motion) In the game, drift is the default movements of objects. The best example is the back and forth 'wave' movement in the lake. This is completely made up. The 'drift' at the microbiology level is called Brownian motion. Brownian motion is a random movement from the collision of particles. Random movement is frustrating and ugly in a video game. Just imaging if the sugar you were going after was randomly moving about, it would be annoying to actually it hit. So, why not just have the molecules sitting there? - It's boring and way more interesting to have things move around. How was the movement decided? - It was made to be similar to the drift that would happen at the macro level. Of course waves in a lake at the micro level would be like tidal waves to bacteria. World Scale The size of the map in the game is 1.6 meters (the size of a large puddle), yet it contains a wide variety of environments. The reason the world is condensed, is it takes around 5 hours to get across, and 5 hours of swimming thru a puddle would be boring, so a variety of environments where condensed together. Dirt/Rocks The changes between the types of dirt (clay, sand, ect), and rocks (sedimentary, igneous, ect), are more drastic than in real life. The placement of different types of rocks and dirt are not 100% accurate, they are semi-accurate though. Friction Friction (or drag) is the force slowing down your bacteria. In some environments, your bacteria can continue moving after the flagella has stopped rotating. But for bacteria, stopping rotation of the flagella most likely ends up with the bacteria stopping. Nutrient Clusters In real life, nutrients are diffused throughout the environment, and rarely meet up as clusters like in the game. The reason nutrients cluster together, is because it's more fun to collect the nutrients up (like PacMan), than have diffused nutrients being absorbed into the cell. It also adds some difficulty into the game. In some early prototypes of the game, nutrients were diffused in the environment, but this alternative play style (nutrient clusters) were more fun. Metal Metabolism In this game, you can metabolize 4 metals which bacteria can't : Gold, Lead, Tin and Copper. and one metaloid Silicon. The option to metabolize these nutrients were added for fun. Scientists are constantly discovering new ways bacteria can metabolize, so adding these metabolism options where to represent possibities of new molecules we may discover bacteria to eat (not that we will find that bacteria eat these exact chemicals, but there is a possibility of finding new chemicals bacteria use). Manganese and Vanadium are two chemicals bacteria use naturaly, but in the game you can extend the use o these nutrients beyond what bacteria naturally use. Naturally, they are commonly used as a co-enzyme, but in the game you can also use these molecules directly to create energy. Redox Tower The redox-tower in the game allows you to customize your metabolism into creating new combinations which are not found normally in nature. Growth Requirment (Carbon) In the game, players must reach a certain size percentage before dividing, the inaccuracy in this, is the game doesn't care which nutrients you collect. For bacteria, it does matter, and the main requirement on bacteria in nature which is not in the game is the requirment of carbon. Of course a carbon requirement could be added to the game, but doing so would limit the possibility (and advantage) to explore different metabolic options (like using metals). Not having a carbon requirement balances out the game for other metabolic options. Carbon Diversity In the game there are 3 nutrients you can collect based on carbon (monosaccharides, disaccharides, and polysaccharides). This of course is completely unrepresentative of the diversity of carbon metabolism found in nature. The reason this variety was left out of the game, was to make room for the alternative metabolic options. But maybe in future expansions of the game, different representations of carbon molecules will be added. Carbon diversity was a feature in early tests of the game, but with the addition of more nutrient types, the carbon variety was simplified as to not make the game overly complex. Tempurature Range The highest tempurature a microbe has been found living in is 121 Celcius. In the game, your bacteria can reach 200 Celcius. The reason for this, is the extremothermophile maximum is constantly being raised to new tempuratures, so why not allow you to pass the known extreme. Nutrient Placement The location of where different nutrients are in respect to different environments are only semi-realistic. The placement of nutirents in different environments was first based on nature, then adjusted to balance the game so a variety of metabolic options were available by mixing the environments together. Secretion Enzymes All secretion enzymes (except Amylase) are made up for the game. Even the concept of secretion enzymes and the how they operate in the game are made up. But of course like everything else in th egame it's based on real microbiology concepts. Environmental Growth Conditions The environmental growth conditions (example tempurature) for bacteria tend to follow a bell-shaped curve (mostly a skewed bell shaped curve), where there is a single maximal condition for maximal growth and the further the environment moves away from this value the more difficult it is for the bacterium to divide (proportionally). Bacillus takes a simplified model where the bacterium has a range, and as long as the bacteria is in this range, it can survive well, but outside the range, it has difficulty.